PhyloRunner is a simple Mac OS X application (written in Applescript) that makes using command line programs easier for command line neophytes. You just double click the application and follow the instructions to select the program you want to run, locate the file, and enter any flags to the program. For example, for r8s, you or your students can run it without having to learn how to navigate in Unix (though you should). The command line programs must be already installed in your system. You can download the program here. People who want to contribute can do so here (the code is GPL3, so you can modify it).
Brownie's installer automatically puts it in the right directory. For others, you can often open the folder containing the source code in terminal, then type
sudo make install;
if "sudo make install" doesn't work, you can just copy the compiled program to a place where it can be run by doing "sudo cp newprogramname /usr/bin".